test classes for dump of results related to funders
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package eu.dnetlib.dhp.oa.graph.dump.funderresult;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.HashMap;
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public class ResultLinkedToProjectTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory
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.getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class);
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private static HashMap<String, String> map = new HashMap<>();
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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public void testNoMatch() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json")
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.getPath();
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final String relationPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json")
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.getPath();
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SparkResultLinkedToProject.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-relationPath", relationPath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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org.apache.spark.sql.Dataset<Result> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Result.class));
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Assertions.assertEquals(0, verificationDataset.count());
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}
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@Test
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public void testMatchOne() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json")
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.getPath();
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final String relationPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json")
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.getPath();
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SparkResultLinkedToProject.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-relationPath", relationPath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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Assertions.assertEquals(1, verificationDataset.count());
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}
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}
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@ -1,4 +1,142 @@
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package eu.dnetlib.dhp.oa.graph.dump.funderresult;
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public class DumpResultPerFunderTest {
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
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import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
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import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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public class SplitPerFunderTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(SplitPerFunderTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(SplitPerFunderTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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public void test1() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump")
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.getPath();
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SparkDumpFunderResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/split",
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"-sourcePath", sourcePath,
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"-relationPath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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// FP7 3
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/split/EC_FP7")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(3, verificationDataset.count());
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Assertions
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.assertEquals(
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1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count());
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// CIHR 2
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tmp = sc
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.textFile(workingDir.toString() + "/split/CIHR")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(2, tmp.count());
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//NWO 1
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tmp = sc
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.textFile(workingDir.toString() + "/split/NWO")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(1, tmp.count());
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//NIH 3
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tmp = sc
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.textFile(workingDir.toString() + "/split/NIH")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(2, tmp.count());
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//NSF 1
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tmp = sc
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.textFile(workingDir.toString() + "/split/NSF")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(1, tmp.count());
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//SNSF 1
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tmp = sc
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.textFile(workingDir.toString() + "/split/SNSF")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(1, tmp.count());
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//NHMRC 1
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tmp = sc
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.textFile(workingDir.toString() + "/split/NHMRC")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(1, tmp.count());
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//H2020 3
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tmp = sc
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.textFile(workingDir.toString() + "/split/EC_H2020")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(3, tmp.count());
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}
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}
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